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MappingQualityZero

Count of all reads with MAPQ = 0 across all samples

Category
Variant Annotations

VCF Field
INFO (variant-level)

Type
StandardAnnotation, ActiveRegionBasedAnnotation

Header info

INFO=

Overview

This anotation gives you the count of all reads that have MAPQ = 0 across all samples. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.